EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 1990, University of Leipzig.
    Habilitation 1995, Humboldt University, Berlin.
    At EMBL since 1991. Head of Unit since 2001.
    Strategic Head of Bioinformatics at EMBL Heidelberg since 2011.
    Group leader in the Molecular Medicine Partnership Unit.
    ERC Advanced Investigator.

Publications

Total: 548 publication(s)

2018

Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Aloy P, Bork P, Gavin AC, Ho AD. (2018)

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline.

Nat Commun 9(1) doi: 10.1038/s41467-018-06353-4
Europe PMC | doi

Bedarf JR, Hildebrand F, Goeser F, Bork P, Wüllner U. (2018)

Das Darmmikrobiom bei der Parkinson-Krankheit.

Nervenarzt doi: 10.1007/s00115-018-0601-6
Europe PMC | doi

Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J. (2018)

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Gut doi: 10.1136/gutjnl-2018-316106
Europe PMC | doi

Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H, Huerta-Cepas J, Medema MH, Maltz MR, Mundra S, Olsson PA, Põlme S, Pent M, Ryberg M, Sunagawa S, Tedersoo L, Bork P. (2018)

Structure and function of the global topsoil microbiome.

Nature 560(7717):233-237. doi: 10.1038/s41586-018-0386-6
Europe PMC | doi

Bahram M, Anslan S, Hildebrand F, Bork P, Tedersoo L. (2018)

Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment.

Environ Microbiol Rep doi: 10.1111/1758-2229.12684
Europe PMC | doi

Kushugulova A, Forslund SK, Costea PI, Kozhakhmetov S, Khassenbekova Z, Urazova M, Nurgozhin T, Zhumadilov Z, Benberin V, Driessen M, Hercog R, Voigt AY, Benes V, Kandels-Lewis S, Sunagawa S, Letunic I, Bork P. (2018)

Metagenomic analysis of gut microbial communities from a Central Asian population.

BMJ Open 8(7) doi: 10.1136/bmjopen-2018-021682
Europe PMC | doi

Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, Armanini F, Truong DT, Manara S, Zolfo M, Beghini F, Bertorelli R, De Sanctis V, Bariletti I, Canto R, Cologna M, Clementi R, Cusumano G, Crifò T, Innamorati C, Gottardi S, Postai D, Masè C, Duranti S, Savoi D, Mancabelli L, Lugli GA, Ferrario C, Turroni F, Mangifesta M, Milani C, Yassour M, Vlamakis H, Anzalone R, Viappiani A, Koren O, Tateo S, Xavier R, Collado CM, Ventura M, Huttenhower C, Soffiati M, Pedrotti A, Bork P, Segata N. (2018)

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.

Cell Host Microbe 24(1):133-145.e5. doi: 10.1016/j.chom.2018.06.005
Europe PMC | doi

Kayser K, Degenhardt F, Holzapfel S, Horpaopan S, Peters S, Spier I, Morak M, Vangala D, Rahner N, von Knebel-Doeberitz M, Schackert HK, Engel C, Büttner R, Wijnen J, Doerks T, Moebus S, Bork P, Fischer S, Herms S, Aretz S, Hoffmann P, Steinke-Lange V. (2018)

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes.

Int. J. Cancer doi: 10.1002/ijc.31725
Europe PMC | doi

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A. (2018)

Species-specific activity of antibacterial drug combinations.

Nature 559(7713):259-263. doi: 10.1038/s41586-018-0278-9
Europe PMC | doi

Parca L, Beck M, Bork P, Ori A. (2018)

Quantifying compartment-associated variations of protein abundance in proteomics data.

Mol. Syst. Biol. 14(7) doi: 10.15252/msb.20178131
Europe PMC | doi

Jones JC, Fruciano C, Marchant J, Hildebrand F, Forslund S, Bork P, Engel P, Hughes WOH. (2018)

The gut microbiome is associated with behavioural task in honey bees.

Insectes Soc 65(3):419-429. doi: 10.1007/s00040-018-0624-9
Europe PMC | doi

Darzi Y, Letunic I, Bork P, Yamada T. (2018)

iPath3.0: interactive pathways explorer v3.

Nucleic Acids Res. 46(W1) doi: 10.1093/nar/gky299
Europe PMC | doi

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM. (2018)

Pervasive Protein Thermal Stability Variation during the Cell Cycle.

Cell 173(6) doi: 10.1016/j.cell.2018.03.053
Europe PMC | doi

Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P. (2018)

Similarity of the dog and human gut microbiomes in gene content and response to diet.

Microbiome 6(1) doi: 10.1186/s40168-018-0450-3
Europe PMC | doi

Rubio-Cosials A, Schulz EC, Lambertsen L, Smyshlyaev G, Rojas-Cordova C, Forslund K, Karaca E, Bebel A, Bork P, Barabas O. (2018)

Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.

Cell 173(1):208-220.e20. doi: 10.1016/j.cell.2018.02.032
Europe PMC | doi

Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. (2018)

Extensive impact of non-antibiotic drugs on human gut bacteria.

Nature 555(7698) doi: 10.1038/nature25979
Europe PMC | doi

Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR. (2018)

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies.

Nat Microbiol 3(4) doi: 10.1038/s41564-018-0123-9
Europe PMC | doi

Schmidt TSB, Raes J, Bork P. (2018)

The Human Gut Microbiome: From Association to Modulation.

Cell 172(6):1198-1215. doi: 10.1016/j.cell.2018.02.044
Europe PMC | doi

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. (2018)

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Nat Microbiol 3(3):388. doi: 10.1038/s41564-018-0114-x
Europe PMC | doi

Korpela K, Costea PI, Coelho LP, Kandels-Lewis S, Willemsen G, Boomsma DI, Segata N, Bork P. (2018)

Selective maternal seeding and environment shape the human gut microbiome.

Genome Res. 28(4) doi: 10.1101/gr.233940.117
Europe PMC | doi

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P. (2018)

A global ocean atlas of eukaryotic genes.

Nat Commun 9(1) doi: 10.1038/s41467-017-02342-1
Europe PMC | doi

Seeleuthner Y, Mondy S, Lombard V, Carradec Q, Pelletier E, Wessner M, Leconte J, Mangot JF, Poulain J, Labadie K, Logares R, Sunagawa S, de Berardinis V, Salanoubat M, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Searson S, Pesant S, Poulton N, Stepanauskas R, Bork P, Bowler C, Hingamp P, Sullivan MB, Iudicone D, Massana R, Aury JM, Henrissat B, Karsenti E, Jaillon O, Sieracki M, de Vargas C, Wincker P. (2018)

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans.

Nat Commun 9(1) doi: 10.1038/s41467-017-02235-3
Europe PMC | doi

Gao NL, Zhang C, Zhang Z, Hu S, Lercher MJ, Zhao XM, Bork P, Liu Z, Chen WH. (2018)

MVP: a microbe-phage interaction database.

Nucleic Acids Res. 46(D1):D700-D707. doi: 10.1093/nar/gkx1124
Europe PMC | doi

Letunic I, Bork P. (2018)

20 years of the SMART protein domain annotation resource.

Nucleic Acids Res. 46(D1):D493-D496. doi: 10.1093/nar/gkx922
Europe PMC | doi

Costea PI, Hildebrand F, Manimozhiyan A, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. (2018)

Enterotypes in the landscape of gut microbial community composition.

Nat Microbiol 3(1):8-16. doi: 10.1038/s41564-017-0072-8
Europe PMC | doi


2017

Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. (2017)

Subspecies in the global human gut microbiome.

Mol. Syst. Biol. 13(12) doi: 10.15252/msb.20177589
Europe PMC | doi

Jones JC, Fruciano C, Hildebrand F, Al Toufalilia H, Balfour NJ, Bork P, Engel P, Ratnieks FL, Hughes WO. (2017)

Gut microbiota composition is associated with environmental landscape in honey bees.

Ecol Evol 8(1):441-451. doi: 10.1002/ece3.3597
Europe PMC | doi

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN. (2017)

Salt-responsive gut commensal modulates TH17 axis and disease.

Nature 551(7682):585-589. doi: 10.1038/nature24628
Europe PMC | doi

Junqueira ACM, Ratan A, Acerbi E, Drautz-Moses DI, Premkrishnan BNV, Costea PI, Linz B, Purbojati RW, Paulo DF, Gaultier NE, Subramanian P, Hasan NA, Colwell RR, Bork P, Azeredo-Espin AML, Bryant DA, Schuster SC. (2017)

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs.

Sci Rep 7(1) doi: 10.1038/s41598-017-16353-x
Europe PMC | doi

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. (2017)

Towards standards for human fecal sample processing in metagenomic studies.

Nat Biotechnol. 35(11) doi: 10.1038/nbt.3960
Europe PMC | doi

Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. (2017)

Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes.

Elife 6 doi: 10.7554/eLife.26066
Europe PMC | doi

Saary P, Forslund K, Bork P, Hildebrand F. (2017)

RTK: efficient rarefaction analysis of large datasets.

Bioinformatics 33(16) doi: 10.1093/bioinformatics/btx206
Europe PMC | doi

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Rinke C, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T. (2017)

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Nat. Biotechnol. 35(8):725-731. doi: 10.1038/nbt.3893
Europe PMC | doi

Huerta-Cepas J, Forslund K, Pedro Coelho L, Szklarczyk D, Juhl Jensen L, von Mering C, Bork P. (2017)

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.

Mol Biol Evol 34(8):2115-2122. doi: 10.1093/molbev/msx148
Europe PMC | doi

Costea PI, Munch R, Coelho LP, Paoli L, Sunagawa S, Bork P. (2017)

metaSNV: A tool for metagenomic strain level analysis.

PLoS One 12(7) doi: 10.1371/journal.pone.0182392
Europe PMC | doi

Kastritis PL, O'Reilly FJ, Bock T, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC. (2017)

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

Mol Syst Biol 13(7):936. doi: 10.15252/msb.20167412
Europe PMC | doi

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. (2017)

Erratum to: Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Genome Med 9(1):61. doi: 10.1186/s13073-017-0451-z
Europe PMC | doi

Bedarf JR, Hildebrand F, Coelho LP, Sunagawa S, Bahram M, Goeser F, Bork P, Wüllner U. (2017)

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.

Genome Med 9(1):1-13. doi: 10.1186/s13073-017-0428-y
Europe PMC | doi

Knoll RL, Forslund K, Kultima JR, Meyer CU, Kullmer U, Sunagawa S, Bork P, Gehring S. (2017)

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition - a metagenomic analysis.

Am. J. Physiol. Gastrointest. Liver Physiol. 312(4):G327-G339. doi: 10.1152/ajpgi.00293.2016
Europe PMC | doi

Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, Parca L, Roth FP, Gavin AC, Bork P, Russell RB. (2017)

Systematic identification of phosphorylation-mediated protein interaction switches.

PLoS Comput. Biol. 13(3):e1005462. doi: 10.1371/journal.pcbi.1005462
Europe PMC | doi

Wang YY, Chen WH, Xiao PP, Xie WB, Luo Q, Bork P, Zhao XM. (2017)

GEAR: A database of Genomic Elements Associated with drug Resistance.

Sci Rep 7(44085):1-8. doi: 10.1038/srep44085
Europe PMC | doi

Jouhten P, Huerta-Cepas J, Bork P, Patil KR. (2017)

Metabolic anchor reactions for robust biorefining.

Metab. Eng. 40:1-4. doi: 10.1016/j.ymben.2017.02.010
Europe PMC | doi

Minguez P, Bork P. (2017)

Bioinformatics Analysis of Functional Associations of PTMs.

Methods Mol. Biol. 1558:303-320. doi: 10.1007/978-1-4939-6783-4_14
Europe PMC | doi

Voigt AY, Zeller G, Bork P. (2017)

[Microbial Biomarkers for Early Cancer Detection].

Dtsch Med Wochenschr 142(4):267-274. doi: 10.1055/s-0042-110193
Europe PMC | doi

Chen WH, Lu G, Chen X, Zhao XM, Bork P. (2017)

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

Nucleic Acids Res. 45(D1):D940-D944. doi: 10.1093/nar/gkw1013
Europe PMC | doi

Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Yong SY, Mitchell AL. (2017)

InterPro in 2017-beyond protein family and domain annotations.

Nucleic Acids Res. 45(D1):D190-D199. doi: 10.1093/nar/gkw1107
Europe PMC | doi

Mende DR, Letunic I, Huerta-Cepas J, Li SS, Forslund K, Sunagawa S, Bork P. (2017)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

Nucleic Acids Res. 45(D1):D529-D534. doi: 10.1093/nar/gkw989
Europe PMC | doi

Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C. (2017)

The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Nucleic Acids Res. 45(D1):D362-D368. doi: 10.1093/nar/gkw937
Europe PMC | doi


2016

Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW. (2016)

Global genetic capacity for mixotrophy in marine picocyanobacteria.

ISME J 10(12):2946-2957. doi: 10.1038/ismej.2016.64
Europe PMC | doi

Scharaw S, Iskar M, Ori A, Boncompain G, Laketa V, Poser I, Lundberg E, Perez F, Beck M, Bork P, Pepperkok R. (2016)

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

J. Cell Biol. 215(4):543-558. doi: 10.1083/jcb.201601090
Europe PMC | doi

Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB. (2016)

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

NATURE 537(7622):689-693. doi: 10.1038/nature19366
Europe PMC | doi

Deghou S, Zeller G, Iskar M, Driessen M, Castillo M, van Noort V, Bork P. (2016)

CART - a chemical annotation retrieval toolkit.

Bioinformatics 32(18):2869-2871. doi: 10.1093/bioinformatics/btw233
Europe PMC | doi

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Dore J, Machado AMD, de Evgrafov MCR, Hansen T, Jorgensen T, Bork P, Guarner F, Pedersen O, Sommer MOA, Ehrlich SD, Sicheritz-Ponten T, Brunak S, Nielsen HB. (2016)

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Nat Microbiol 1(11):16152. doi: 10.1038/nmicrobiol.2016.152
Europe PMC | doi

Kultima JR, Coelho LP, Forslund K, Huerta-Cepas J, Li SS, Driessen M, Voigt AY, Zeller G, Sunagawa S, Bork P. (2016)

MOCAT2: a metagenomic assembly, annotation and profiling framework.

Bioinformatics 32(16):2520-2523. doi: 10.1093/bioinformatics/btw183
Europe PMC | doi

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K, Consortium M, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O. (2016)

Human gut microbes impact host serum metabolome and insulin sensitivity.

Nature 535(535):376-381. doi: 10.1038/nature18646
Europe PMC | doi

Letunic I, Bork P. (2016)

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Nucleic Acids Res. 44(W1):W242-W245. doi: 10.1093/nar/gkw290
Europe PMC | doi

Huerta-Cepas J, Serra F, Bork P. (2016)

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.

Mol. Biol. Evol. 33(6):1635-1638. doi: 10.1093/molbev/msw046
Europe PMC | doi

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC. (2016)

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Nat Protoc 11(6):1021-1038. doi: 10.1038/nprot.2016.059
Europe PMC | doi

Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R. (2016)

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

PLoS ONE 11(5):e0155362. doi: 10.1371/journal.pone.0155362
Europe PMC | doi

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. (2016)

Standardized benchmarking in the quest for orthologs.

Nat. Methods 13(5):425-430. doi: 10.1038/nmeth.3830
Europe PMC | doi

Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Nieuwdorp M, Salojärvi J, Voigt AY, Zeller G, Sunagawa S, de Vos WM, Bork P. (2016)

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

Science 352(6285):586-589. doi: 10.1126/science.aad8852
Europe PMC | doi

Chen WH, Lu G, Bork P, Hu S, Lercher MJ. (2016)

Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

Nat Commun 7 doi: 10.1038/ncomms11334
Europe PMC | doi

Cornejo-Castillo FM, Cabello AM, Salazar G, Sanchez-Baracaldo P, Lima-Mendez G, Hingamp P, Alberti A, Sunagawa S, Bork P, de Vargas C, Raes J, Bowler C, Wincker P, Zehr JP, Gasol JM, Massana R, Acinas SG. (2016)

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.

NAT COMMUN 7 doi: 10.1038/ncomms11071
Europe PMC | doi

Ori A, Iskar M, Buczak K, Kastritis P, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M. (2016)

Spatiotemporal variation of mammalian protein complex stoichiometries.

Genome Biol. 17(1) doi: 10.1186/s13059-016-0912-5
Europe PMC | doi

Noguera-Julian M, Rocafort M, Guillén Y, Rivera J, Casadellà M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, Rodríguez C, Carrillo J, Mothe B, Coll J, Bravo I, Estany C, Herrero C, Saz J, Sirera G, Torrela A, Navarro J, Crespo M, Brander C, Negredo E, Blanco J, Guarner F, Calle ML, Bork P, Sönnerborg A, Clotet B, Paredes R. (2016)

Gut Microbiota Linked to Sexual Preference and HIV Infection.

EBioMedicine 5:135-146. doi: 10.1016/j.ebiom.2016.01.032
Europe PMC | doi

Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar M. (2016)

Bacterial antisense RNAs are mainly the product of transcriptional noise.

Sci Adv 2(3) doi: 10.1126/sciadv.1501363
Europe PMC | doi

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JC, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Tara Oceans Consortium Coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. (2016)

Plankton networks driving carbon export in the oligotrophic ocean.

Nature 532(7600) doi: 10.1038/nature16942
Europe PMC | doi

Zhang XD, Song J, Bork P, Zhao XM. (2016)

The exploration of network motifs as potential drug targets from post-translational regulatory networks.

Sci Rep 6 doi: 10.1038/srep20558
Europe PMC | doi

Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM. (2016)

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.

Nat Commun 7 doi: 10.1038/ncomms10410
Europe PMC | doi

Chen WH, van Noort V, Lluch-Senar M, Hennrich ML, H Wodke JA, Yus E, Alibés A, Roma G, Mende DR, Pesavento C, Typas A, Gavin AC, Serrano L, Bork P. (2016)

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.

Nucleic Acids Res. 44(3) doi: 10.1093/nar/gkw004
Europe PMC | doi

Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis P, Bork P, Beck M, Müller CW. (2016)

The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.

PLoS ONE 11(1) doi: 10.1371/journal.pone.0146457
Europe PMC | doi

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. (2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.

Nucleic Acids Res 44(D1):D286-D293. doi: 10.1093/nar/gkv1248
Europe PMC | doi

Kuhn M, Letunic I, Jensen LJ, Bork P. (2016)

The SIDER database of drugs and side effects.

Nucleic Acids Res 44(D1):D1075-9. doi: 10.1093/nar/gkv1075
Europe PMC | doi

Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M. (2016)

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.

Nucleic Acids Res. 44(D1):D380-D384. doi: 10.1093/nar/gkv1277
Europe PMC | doi


2015

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Krogh Pedersen H, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Igor Costea P, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J, MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O. (2015)

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Nature 528(7581):262-266. doi: 10.1038/nature15766
Europe PMC | doi

Shieh YW, Minguez P, Bork P, Auburger JJ, Guilbride DL, Kramer G, Bukau B. (2015)

Operon structure and cotranslational subunit association direct protein assembly in bacteria.

Science 350(6261) doi: 10.1126/science.aac8171
Europe PMC | doi

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. (2015)

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.

Cell Sys 1(3):224-237. doi: 10.1016/j.cels.2015.08.012
Europe PMC | doi

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M. (2015)

In situ structural analysis of the human nuclear pore complex.

Nature 526(7571):140-143. doi: 10.1038/nature15381
Europe PMC | doi

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC. (2015)

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Cell Rep 12(9):1519-1530. doi: 10.1016/j.celrep.2015.07.054
Europe PMC | doi

Zhang C, Yin A, Li H, Wang R, Wu G, Shen J, Zhang M, Wang L, Hou Y, Ouyang H, Zhang Y, Zheng Y, Wang J, Lv X, Wang Y, Zhang F, Zeng B, Li W, Yan F, Zhao Y, Pang X, Zhang X, Fu H, Chen F, Zhao N, Hamaker BR, Bridgewater LC, Weinkove D, Clement K, Dore J, Holmes E, Xiao H, Zhao G, Yang S, Bork P, Nicholson JK, Wei H, Tang H, Zhang X, Zhao L. (2015)

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.

EBioMedicine 2(8):966-982. doi: 10.1016/j.ebiom.2015.07.007
Europe PMC | doi

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T. (2015)

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

Genome Biol. Evol. 7(7):1988-1999. doi: 10.1093/gbe/evv121
Europe PMC | doi

Bork P, Bowler C, de Vargas C, Gorsky G, Karsenti E, Wincker P. (2015)

Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction.

Science 348(6237) doi: 10.1126/science.aac5605
Europe PMC | doi

Sunagawa S, Karsenti E, Bowler C, Bork P. (2015)

Computational eco-systems biology in Tara Oceans: translating data into knowledge.

Mol. Syst. Biol. 11(5) doi: 10.15252/msb.20156272
Europe PMC | doi

Tedersoo L, Anslan S, Bahram M, Polme S, Riit T, Liiv I, Koljalg U, Kisand V, Nilsson RH, Hildebrand F, Bork P, Abarenkov K. (2015)

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi.

MycoKeys (10):1-43. doi: 10.3897/mycokeys.10.4852
doi

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR. (2015)

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Proc. Natl. Acad. Sci. U.S.A. 112(20):6449-6454. doi: 10.1073/pnas.1421834112
Europe PMC | doi

Brum JR, Ignacio-Espinoza JC, Roux S, Doulcier G, Acinas SG, Alberti A, Chaffron S, Cruaud C, de Vargas C, Gasol JM, Gorsky G, Gregory AC, Guidi L, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Poulos BT, Schwenck SM, Speich S, Dimier C, Kandels-Lewis S, Picheral M, Searson S, Tara Oceans Coordinators, Bork P, Bowler C, Sunagawa S, Wincker P, Karsenti E, Sullivan MB. (2015)

Ocean plankton. Patterns and ecological drivers of ocean viral communities.

Science 348(6237) doi: 10.1126/science.1261498
Europe PMC | doi

de Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horák A, Jaillon O, Lima-Mendez G, Lukeš J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E. (2015)

Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.

Science 348(6237) doi: 10.1126/science.1261605
Europe PMC | doi

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J. (2015)

Ocean plankton. Determinants of community structure in the global plankton interactome.

Science 348(6237) doi: 10.1126/science.1262073
Europe PMC | doi

Mackmull MT, Iskar M, Parca L, Singer S, Bork P, Ori A, Beck M. (2015)

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

Mol. Cell Proteomics 14(5) doi: 10.1074/mcp.m114.042499
Europe PMC | doi

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. (2015)

Ocean plankton. Structure and function of the global ocean microbiome.

Science 348(6237) doi: 10.1126/science.1261359
Europe PMC | doi

Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D. (2015)

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Science 348(6237) doi: 10.1126/science.1261447
Europe PMC | doi

Zhu A, Sunagawa S, Mende DR, Bork P. (2015)

Inter-individual differences in the gene content of human gut bacterial species.

Genome Biol. 16(1) doi: 10.1186/s13059-015-0646-9
Europe PMC | doi

Voigt AY, Costea PI, Kultima JR, Li SS, Zeller G, Sunagawa S, Bork P. (2015)

Temporal and technical variability of human gut metagenomes.

Genome Biol. 16(1) doi: 10.1186/s13059-015-0639-8
Europe PMC | doi

Betts MJ, Lu Q, Jiang Y, Drusko A, Wichmann O, Utz M, Valtierra-Gutiérrez IA, Schlesner M, Jaeger N, Jones DT, Pfister S, Lichter P, Eils R, Siebert R, Bork P, Apic G, Gavin AC, Russell RB. (2015)

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

Nucleic Acids Res. 43(2):e10. doi: 10.1093/nar/gku1094
Europe PMC | doi

Lluch-Senar M, Delgado J, Chen WH, Lloréns-Rico V, O'Reilly FJ, Wodke JA, Unal EB, Yus E, Martínez S, Nichols RJ, Ferrar T, Vivancos A, Schmeisky A, Stülke J, van Noort V, Gavin AC, Bork P, Serrano L. (2015)

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Mol. Syst. Biol. 11(1) doi: 10.15252/msb.20145558
Europe PMC | doi

Letunic I, Doerks T, Bork P. (2015)

SMART: recent updates, new developments and status in 2015.

Nucleic Acids Res. 43(D1) doi: 10.1093/nar/gku949
Europe PMC | doi

Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P. (2015)

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.

Nucleic Acids Res. 43(D1) doi: 10.1093/nar/gku1081
Europe PMC | doi

Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. (2015)

The InterPro protein families database: the classification resource after 15 years.

Nucleic Acids Res. 43(D1) doi: 10.1093/nar/gku1243
Europe PMC | doi

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerte-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. (2015)

STRING v10: protein-protein interaction networks, integrated over the tree of life.

Nucleic Acids Res. 43(D1) doi: 10.1093/nar/gku1003
Europe PMC | doi


2014

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P. (2014)

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Nucleic Acids Res. 42(22):13525-13533. doi: 10.1093/nar/gku1147
Europe PMC | doi